Comparative virulence and antimicrobial resistance distribution of Streptococcus suis isolates obtained from the United States

Abstract

Streptococcus suis is a zoonotic bacterial swine pathogen causing substantial economic and health burdens to the pork industry worldwide. Most S. suis genome sequences available in public databases are from isolates obtained outside the United States. We sequenced the genomes of 106 S. suis isolates from the U.S. and analyzed them to identify their potential to function as zoonotic agents and/or reservoirs for antimicrobial resistance (AMR) dissemination. The objective of this study was to evaluate the genetic diversity of S. suis isolates obtained within the U.S., for the purpose of screening for genomic elements encoding AMR and any factors that could increase or contribute to the capacity of S. suis to transmit, colonize, and/or cause disease in humans. Forty-six sequence types (STs) were identified with ST28 observed as the most prevalent, followed by ST87. Of the 23 different serotypes identified, serotype 2 was the most prevalent, followed by serotype 8 and 3. Of the virulence genes analyzed, the highest nucleotide diversity was observed in sadP, mrp, and ofs. Tetracycline resistance was the most prevalent phenotypic antimicrobial resistance observed followed by macrolide-lincosamide-streptogramin B (MLSB) resistance. Numerous AMR elements were identified, many located within MGE sequences, with the highest frequency observed for ble, tetO and ermB. No genes encoding factors known to contribute to the transmission, colonization, and/or causation of disease in humans were identified in any of the S. suis genomes in this study. This includes the 89 K pathogenicity island carried by the virulent S. suis isolates responsible for human infections. Collectively, the data reported here provide a comprehensive evaluation of the genetic diversity among U.S. S. suis isolates. This study also serves as a baseline for determining any potential risks associated with occupational exposure to these bacteria, while also providing data needed to address public health concerns.

Keywords: Streptococcus suis; antimicrobial resistance; comparative genomics; mobile genetic elements; swine; virulence; whole-genome sequencing.

Figure 1

AMR gene frequency among Streptococcus suis isolates. The x axis indicates the number of AMR genes harbored by a single isolate. The y axis indicates the number of isolates identified harboring each number of AMR genes.

Figure 2

Genomic organization and alignment of the region containing the lsaE, lnuB, ant(6)-Ia, and ant(9)-Ia genes. The S. suis isolate and contig number (c) for each sequence, along with the accession number for the Enterococcus faecium plasmid shown at right. Base pair numbers are displayed above black bar at top. Green and yellow shaded bar below depicts sequence similarity with green indicating 100% identity and yellow indicating lower identity. Grey bar in between each aligned sequence region depicts sequence similarity between each sequence with grey indicating nucleotide positions with 100% identity. Blue arrows at end of grey bars indicate contig sequence continues. AMR gene elements are listed below and indicated by green (lsaE), yellow (lnuB), orange (ant(6)-Ia), and pink (ant(9)-Ia) genes. All other CDSs are indicated by light blue. The ant(6)-Ia gene in 40529 c2 is a partial gene (missing N-terminus) and is flagged as predicted pseudogene by PGAP. Accession number CP040850 is a complete nucleotide sequence from an Enterococcus faecium strain F17E0263 plasmid (p_unnamed1) isolated from a chicken.

Figure 3

Genomic organization and alignment of the region containing the ant(6)-Ia, sat4, and aph(3′)-IIIa genes. The S. suis isolate and contig number (c) for each sequence, along with the accession numbers for the Enterococcus faecium plasmid and the Erysipelothrix rhusiopathiae ICE (ICCEr0106) shown at right. Base pair numbers are displayed above black bar at top. Green and yellow shaded bar below depicts sequence identity with green indicating 100% identity and yellow indicating lower identity. Grey bar in between each aligned sequence region depicts sequence similarity between each sequence with grey indicating nucleotide positions with 100% identity. Blue arrows at end of grey bars indicate contig sequence continues and orange bars indicate end of contig sequence. AMR gene elements are listed below and are indicated by orange (ant(6)-Ia), pink (ant(9)-Ia), green (lsaE), yellow (lnuB), red (ant(6)-Ia), purple (sat4), and dark blue (aph(3′)-IIIa). All other CDSs are indicated by light blue. Predicted incomplete CDSs are indicated by jagged ends. Accession number MG957432 is a complete nucleotide sequence from Enterococcus faecium strain 37BA conjugative plasmid (pEf37BA) isolated from a human. Accession number MG812141 is a complete nucleotide sequence from Erysipelothrix rhusiopathiae ICE (ICCEr0106).

Figure 4

Genomic organization and alignment of the region containing the vgb and vat genes. The S. suis isolate and contig number (c) for each sequence, along with the accession number for the S. suis phage phi-SsuFJNP3_rum shown at right. Base pair numbers are displayed above the black bar at top. Green and yellow shaded bar below depicts sequence similarity with green indicating 100% identity and yellow indicating lower identity. Grey bar in between each aligned sequence region depicts sequence similarity between each sequence with grey indicating nucleotide positions with 100% identity. Blue arrows at end of grey bars indicate contig sequence continues and orange bars indicate end of contig sequence. AMR gene elements are listed below and indicated by pink (vgb) and yellow (vat). All other CDSs are indicated by light blue. Predicted incomplete CDSs are indicated by jagged ends. Accession number MN270260 is a complete nucleotide sequence from S. suis phage phi-SsuFJNP3_rum harbored by S. suis strain PJNP3, isolated from a pig.

Figure 5

Hierarchical cluster heatmap displaying the relatedness of S. suis isolates based on the nucleotide percent identity of analyzed virulence genes. A distance matrix generated form the nucleotide percentage identity was converted into a heatmap and clustered by means of complete hierarchical clustering based on Pearson correlation distance for both genes and isolates. Gene names are provided at the top of the heat map and isolate names along with their corresponding CC are provided at the right side of heat map. Percent identity of analyzed genes (columns) from each isolate (rows) is represented using the color scale at top, while genes not present within an isolate are indicated by grey. Dendrograms are on the left side and on top of the heat map.